1. Web clipper, which I use as a bookmark replacement, as well as for keeping copies of articles. Great for searching and knowing that I will always have a copy if a site suddenly disappears.
2. PDF ocr / search. I store a lot of receipts, contracts, invoices, manuals and other docs in Evernote, most of which are in PDF. I find the search-in-pdf feature indispensable.
I would love to move to something simpler like Bear (http://www.bear-writer.com), which has a superior writing experience. However, the two points above always make me come back to Evernote.
Edit: Also forgot to include the ability to take unstructured notes and sketches using the Apple Pencil on an iPad, while a bit cumbersome in Evernote, at least works.